Ratiometric gas reporting: a non-disruptive approach to monitor gene expression in soils.

Fluorescent proteins are ubiquitous tools that are used to monitor the dynamic functions of natural and synthetic genetic circuits. However, these visual reporters can only be used in transparent settings, a limitation that complicates non-disruptive measurements of gene expression within many matrices, such as soils and sediments. We describe a new ratiometric gas reporting method for non-disruptively monitoring gene expression within hard-to-image environmental matrices. With this approach, CH is continuously synthesized by ethylene forming enzyme to provide information on viable cell number, and CHBr is conditionally synthesized by placing a methyl halide transferase gene under the control of a conditional promoter. We show that ratiometric gas reporting enables the creation of Escherichia coli biosensors that report on acylhomoserine lactone (AHL) autoinducers used for quorum sensing by gram-negative bacteria. Using these biosensors, we find that an agricultural soil decreases the bioavailable concentration of a long-chain AHL up to 100-fold. We also demonstrate that these biosensors can be used in soil to non-disruptively monitor AHLs synthesized by Rhizobium leguminosarum and degraded by Bacillus thuringiensis. Finally, we show that this new reporting approach can be used in Shewanella oneidensis, a bacterium that lives in sediments.